Molecular, clinical and therapeutic determinants of outcome in NPM1 mutated AML.

Although NPM1-mutated acute myeloid leukemia (AML) carries a generally favorable prognosis, many patients still relapse and die. Previous studies identified several molecular and clinical features associated with poor outcome, however only FLT3-ITD mutation and adverse karyotype are currently used for risk stratification due to inconsistent results and uncertainty around how other factors should influence treatment, particularly given the strong prognostic impact of post-induction measurable residual disease (MRD). Here we analyzed a large group of patients with NPM1mut AML enrolled in prospective trials (NCRI AML17 and AML19, n=1357) to delineate the impact of baseline molecular and clinical features, post induction MRD status and treatment intensity on outcome. FLT3-ITD (HR 1.28, 95%CI 1.01-1.63), DNMT3A (HR 1.65, 95%CI 1.32-2.05), WT1 (HR 1.74, 95%CI 1272-2.38) and non-ABD NPM1 mutations (HR 1.64, 95%CI 1.22-2.21) were independently associated with poorer overall survival (OS). These factors were also strongly associated with MRD positivity. For patients achieving MRD negativity, these mutations (except FLT3-ITD) were associated with an increased cumulative incidence of relapse (CIR) and poorer OS. However, apart from the few patients with adverse cytogenetics, we could not identify any group of MRD negative patients with a CIR >40% or with benefit from allograft in first remission. Intensified chemotherapy with the FLAG-Ida regimen was associated with improved outcomes in all subgroups, with greater benefits observed in the highest risk molecular subgroups.

Computational scoring and experimental evaluation of enzymes generated by neural networks.

In recent years, generative protein sequence models have been developed to sample novel sequences. However, predicting whether generated proteins will fold and function remains challenging. We evaluate a set of 20 diverse computational metrics to assess the quality of enzyme sequences produced by three contrasting generative models: ancestral sequence reconstruction, a generative adversarial network and a protein language model. Focusing on two enzyme families, we expressed and purified over 500 natural and generated sequences with 70-90% identity to the most similar natural sequences to benchmark computational metrics for predicting in vitro enzyme activity. Over three rounds of experiments, we developed a computational filter that improved the rate of experimental success by 50-150%. The proposed metrics and models will drive protein engineering research by serving as a benchmark for generative protein sequence models and helping to select active variants for experimental testing.

Watch Me Play!: protocol for a feasibility study of a remotely delivered intervention to promote mental health resilience for children (ages 0-8) across UK early years and children's services.

BACKGROUND: Half of mental health problems are established by the age of 14 years and 75% by 24 years. Early intervention and prevention of mental ill health are therefore vitally important. However, increased demand over recent years has meant that access to child mental health services is often restricted to those in severest need. Watch Me Play! (WMP) is an early intervention designed to support caregiver attunement and attention to the child to promote social-emotional well-being and thereby mental health resilience. Originally developed in the context of a local authority mental health service for children in care, it is now also delivered online as a low intensity, scalable, preventative intervention. Although WMP shows promise and is already used in some services, we do not yet know whether it is effective. METHODS: A non-randomised single group feasibility study with embedded process evaluation. We propose to recruit up to 40 parents/carers of children aged 0-8 years who have been referred to early years and children's services in the UK. WMP involves a parent watching the child play and talking to their child about their play (or for babies, observing and following signals) for up to 20 min per session. Some sessions are facilitated by a trained practitioner who provides prompts where necessary, gives feedback, and discusses the child's play with the caregiver. Services will offer five facilitated sessions, and parents will be asked to do at least 10 additional sessions on their own with their child in a 5-week period. Feasibility outcomes examined are as follows: (i) recruitment, (ii) retention, (iii) adherence, (iv) fidelity of delivery, (v) barriers and facilitators of participation, (vi) intervention acceptability, (vii) description of usual care, and (viii) data collection procedures. Intervention mechanisms will be examined through qualitative interview data. Economic evaluation will be conducted estimating cost of the intervention and cost of service use for child and parents/carers quality-adjusted life years. DISCUSSION: This study will address feasibility questions associated with progression to a future randomised trial of WMP. TRIAL REGISTRATION: ISRCTN13644899 . Registered on 14th April 2023.

Sensitive remote homology search by local alignment of small positional embeddings from protein language models.

Accurately detecting distant evolutionary relationships between proteins remains an ongoing challenge in bioinformatics. Search methods based on primary sequence struggle to accurately detect homology between sequences with less than 20% amino acid identity. Profile- and structure-based strategies extend sensitive search capabilities into this twilight zone of sequence similarity but require slow pre-processing steps. Recently, whole-protein and positional embeddings from deep neural networks have shown promise for providing sensitive sequence comparison and annotation at long evolutionary distances. Embeddings are generally faster to compute than profiles and predicted structures but still suffer several drawbacks related to the ability of whole-protein embeddings to discriminate domain-level homology, and the database size and search speed of methods using positional embeddings. In this work, we show that low-dimensionality positional embeddings can be used directly in speed-optimized local search algorithms. As a proof of concept, we use the ESM2 3B model to convert primary sequences directly into the 3D interaction (3Di) alphabet or amino acid profiles and use these embeddings as input to the highly optimized Foldseek, HMMER3, and HH-suite search algorithms. Our results suggest that positional embeddings as small as a single byte can provide sufficient information for dramatically improved sensitivity over amino acid sequence searches without sacrificing search speed.

Highly Parallelized Construction of DNA from Low-Cost Oligonucleotide Mixtures Using Data-Optimized Assembly Design and Golden Gate.

Commercially synthesized genes are typically made using variations of homology-based cloning techniques, including polymerase cycling assembly from chemically synthesized microarray-derived oligonucleotides. Here, we apply Data-optimized Assembly Design (DAD) to the synthesis of hundreds of codon-optimized genes in both constitutive and inducible vectors using Golden Gate Assembly. Starting from oligonucleotide pools, we synthesize genes in three simple steps: (1) amplification of parts belonging to individual assemblies in parallel from a single pool; (2) Golden Gate Assembly of parts for each construct; and (3) transformation. We construct genes from receiving DNA to sequence confirmed isolates in as little as 4 days. By leveraging the ligation fidelity afforded by T4 DNA ligase, we expect to be able to construct a larger breadth of sequences not currently supported by homology-based methods, which require stability of extensive single-stranded DNA overhangs.

Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme.

Deaminases have important uses in modification detection and genome editing. However, the range of applications is limited by the small number of characterized enzymes. To expand the toolkit of deaminases, we developed an in vitro approach that bypasses a major hurdle with their toxicity in cells. We assayed 175 putative cytosine deaminases on a variety of substrates and found a broad range of activity on double- and single-stranded DNA in various sequence contexts, including CpG-specific deaminases and enzymes without sequence preference. We also characterized enzyme selectivity across six DNA modifications and reported enzymes that do not deaminate modified cytosines. The detailed analysis of diverse deaminases opens new avenues for biotechnological and medical applications. As a demonstration, we developed SEM-seq, a non-destructive single-enzyme methylation sequencing method using a modification-sensitive double-stranded DNA deaminase. The streamlined protocol enables accurate, base-resolution methylome mapping of scarce biological material, including cell-free DNA and 10 pg input DNA.

Postinduction molecular MRD identifies patients with NPM1 AML who benefit from allogeneic transplant in first remission.

ABSTRACT: Selection of patients with NPM1-mutated acute myeloid leukemia (AML) for allogeneic transplant in first complete remission (CR1-allo) remains controversial because of a lack of robust data. Consequently, some centers consider baseline FLT3-internal tandem duplication (ITD) an indication for transplant, and others rely on measurable residual disease (MRD) status. Using prospective data from the United Kingdom National Cancer Research Institute AML17 and AML19 studies, we examined the impact of CR1-allo according to peripheral blood NPM1 MRD status measured by quantitative reverse transcription polymerase chain reaction after 2 courses of induction chemotherapy. Of 737 patients achieving remission, MRD was positive in 19%. CR1-allo was performed in 46% of MRD+ and 17% of MRD- patients. We observed significant heterogeneity of overall survival (OS) benefit from CR1-allo according to MRD status, with substantial OS advantage for MRD+ patients (3-year OS with CR1-allo vs without: 61% vs 24%; hazard ratio [HR], 0.39; 95% confidence interval [CI], 0.24-0.64; P < .001) but no benefit for MRD- patients (3-year OS with CR1-allo vs without: 79% vs 82%; HR, 0.82; 95% CI, 0.50-1.33; P = .4). Restricting analysis to patients with coexisting FLT3-ITD, again CR1-allo only improved OS for MRD+ patients (3-year OS, 45% vs 18%; compared with 83% vs 76% if MRD-); no interaction with FLT3 allelic ratio was observed. Postinduction molecular MRD reliably identifies those patients who benefit from allogeneic transplant in first remission. The AML17 and AML19 trials were registered at www.isrctn.com as #ISRCTN55675535 and #ISRCTN78449203, respectively.

Digital adaptation of the Standing up for Myself intervention in young people and adults with intellectual disabilities: the STORM feasibility study.

Background: Stigma contributes to the negative social conditions persons with intellectual disabilities are exposed to, and it needs tackling at multiple levels. Standing Up for Myself is a psychosocial group intervention designed to enable individuals with intellectual disabilities to discuss stigmatising encounters in a safe and supportive setting and to increase their self-efficacy in managing and resisting stigma. Objectives: To adapt Standing Up for Myself to make it suitable as a digital intervention; to evaluate the feasibility and acceptability of Digital Standing Up for Myself and online administration of outcome measures in a pilot; to describe usual practice in the context of the coronavirus disease 2019 pandemic to inform future evaluation. Design: Adaptation work followed by a single-arm pilot of intervention delivery. Setting and participants: Four third and education sector organisations. Individuals with mild-to-moderate intellectual disabilities, aged 16+, members of existing groups, with access to digital platforms. Intervention: Digital Standing Up for Myself intervention. Adapted from face-to-face Standing Up for Myself intervention, delivered over four weekly sessions, plus a 1-month follow-up session. Outcomes: Acceptability and feasibility of delivering Digital Standing Up for Myself and of collecting outcome and health economic measures at baseline and 3 months post baseline. Outcomes are mental well-being, self-esteem, self-efficacy in rejecting prejudice, reactions to discrimination and sense of social power. Results: Adaptation to the intervention required changes to session duration, group size and number of videos; otherwise, the content remained largely the same. Guidance was aligned with digital delivery methods and a new group member booklet was produced. Twenty-two participants provided baseline data. The intervention was started by 21 participants (four groups), all of whom were retained at 3 months. Group facilitators reported delivering the intervention as feasible and suggested some refinements. Fidelity of the intervention was good, with over 90% of key components observed as implemented by facilitators. Both facilitators and group members reported the intervention to be acceptable. Group members reported subjective benefits, including increased confidence, pride and knowing how to deal with difficult situations. Digital collection of all outcome measures was feasible and acceptable, with data completeness ≥ 95% for all measures at both time points. Finally, a picture of usual practice has been developed as an intervention comparator for a future trial. Limitations: The pilot sample was small. It remains unclear whether participants would be willing to be randomised to a treatment as usual arm or whether they could be retained for 12 months follow-up. Conclusions: The target number of groups and participants were recruited, and retention was good. It is feasible and acceptable for group facilitators with some training and supervision to deliver Digital Standing Up for Myself. Further optimisation of the intervention is warranted. Future work: To maximise the acceptability and reach of the intervention, a future trial could offer the adapted Digital Standing Up for Myself, potentially alongside the original face-to-face version of the intervention. Study registration: This study was registered as ISRCTN16056848. Funding: This award was funded by the National Institute for Health and Care Research (NIHR) Public Health Research programme (NIHR award ref: 17/149/03) and is published in full in Public Health Research; Vol. 12, No. 1. See the NIHR Funding and Awards website for further award information.

People with intellectual disabilities (or 'learning disabilities' in United Kingdom language) are more likely to experience poor physical and mental health than the general population. Stigma (negative stereotypes, prejudice and discrimination) has been linked to lower self-esteem, quality of life, and mental and physical ill health. Efforts to empower people with intellectual disabilities themselves to challenge stigma with a view to improving well-being, health and self-esteem are lacking. In 2017, we developed Standing Up for Myself, a brief group-based programme for people with mild-to-moderate intellectual disabilities aged 16+ to address this gap. As this study got underway, face-to-face meetings were suspended due to the coronavirus disease 2019 pandemic. We used the opportunity to assess whether Standing Up for Myself could be delivered through web-based meetings. We adapted Standing Up for Myself for digital delivery, with close input from advisors with intellectual disabilities and experienced group facilitators. We then tested the digital version in charity and education settings to evaluate if Digital Standing Up for Myself could be delivered as planned and how acceptable it was to group facilitators and participants. Four groups, with a total of 22 members, signed up to try Digital Standing Up for Myself. One participant dropped out before starting Standing Up for Myself, and the other 21 continued until the end of the programme. Retention and attendance were good; participants on average attended four of the five sessions. Ninety per cent of the core programme requirements were fully delivered as detailed in the Digital Standing Up for Myself manual. Problems with technology were manageable, although facilitators found using the Standing Up for Myself Wiki platform (an online platform for storage and sharing of resources) difficult, particularly when sharing video content. Facilitators felt acceptable levels of privacy were achieved and there were no reports of undue distress. All facilitators and many group members said they would recommend Digital Standing Up for Myself to others. Group members shared how the programme benefitted them, noting increased awareness about disabilities, and for some increased confidence, pride and independence. Some had learnt how to stand up for themselves and manage difficult situations and took pride in this. Completing outcome and health cost measures via web-based meetings was acceptable and data were largely fully complete and useable.

Epidemiology of Gender Diversity.

In the United States, approximately 1.6 million individuals identify as transgender and gender diverse (TGD), encompassing a wide range of identities and experiences. Despite progress in visibility and acceptance, TGD people continue to face health care and societal disparities, especially affecting racial minorities. Although legal advancements have been achieved, the key to addressing these persistent health care disparities lies in implementing comprehensive and culturally sensitive health care practices and supportive policies. With a growing number of TGD people seeking gender-affirming care, it is imperative that health care practitioners understand the unique challenges faced by this community and provide tailored services with sensitivity and expertise.

Conserved Residues at the Mtr4 C-Terminus Coordinate Helicase Activity and Exosome Interactions.

Mtr4 is an essential RNA helicase involved in nuclear RNA processing and degradation and is a member of the Ski2-like helicase family. Ski2-like helicases share a common core architecture that includes two RecA-like domains, a winged helix, and a helical bundle (HB) domain. In Mtr4, a short C-terminal tail immediately follows the HB domain and is positioned at the interface of the RecA-like domains. The tail ends with a SLYΦ sequence motif that is highly conserved in a subset of Ski2-like helicases. Here, we show that this sequence is critical for Mtr4 function. Mutations in the C-terminus result in decreased RNA unwinding activity. Mtr4 is a key activator of the RNA exosome complex, and mutations in the SLYΦ motif produce a slow growth phenotype when combined with a partial exosome defect in S. cerevisiae, suggesting an important role of the C-terminus of Mtr4 and the RNA exosome. We further demonstrate that C-terminal mutations impair RNA degradation activity by the major RNA exosome nuclease Rrp44 in vitro. These data demonstrate a role for the Mtr4 C-terminus in regulating helicase activity and coordinating Mtr4-exosome interactions.

Protease-Activated Receptor 2 Controls Vascular Smooth Muscle Cell Proliferation in Cyclic AMP-Dependent Protein Kinase/Mitogen-Activated Protein Kinase Kinase 1/2-Dependent Manner.

INTRODUCTION: Cardiovascular disorders are characterized by vascular smooth muscle (VSM) transition from a contractile to proliferative state. Protease-activated receptor 2 (PAR2) involvement in this phenotypic conversion remains unclear. We hypothesized that PAR2 controls VSM cell proliferation in phenotype-dependent manner and through specific protein kinases. METHODS: Rat clonal low (PLo; P3-P6) and high passage (PHi; P10-P15) VSM cells were established as respective models of quiescent and proliferative cells, based on reduced PKG-1 and VASP. Western blotting determined expression of cytoskeletal/contractile proteins, PAR2, and select protein kinases. DNA synthesis and cell proliferation were measured 24-72 h following PAR2 agonism (SLIGRL; 100 nM-10 µm) with/without PKA (PKI; 10 µm), MEK1/2 (PD98059; 10 µm), and PI3K (LY294002; 1 µm) blockade. RESULTS: PKG-1, VASP, SM22α, calponin, cofilin, and PAR2 were reduced in PHi versus PLo cells. Following PAR2 agonism, DNA synthesis and cell proliferation increased in PLo cells but decreased in PHi cells. Western analyses showed reduced PKA, MEK1/2, and PI3K in PHi versus PLo cells, and kinase blockade revealed PAR2 controls VSM cell proliferation through PKA/MEK1/2. DISCUSSION: Findings highlight PAR2 and PAR2-driven PKA/MEK1/2 in control of VSM cell growth and provide evidence for continued investigation of PAR2 in VSM pathology.

Comparing the Accuracy of Mini-BAL to Bronchoscopic BAL in the Diagnosis of Pneumonia Among Ventilated Patients: A Systematic Literature Review.

Background: Despite its widespread use, there are no direct studies comparing mini-bronchoalveolar lavage (mini-BAL) to bronchoscopic bronchoalveolar lavage (BAL) for diagnosing pneumonia in ventilated patients. The aim of this study was to perform a systematic review of studies comparing ventilated patients undergoing both bronchoscopic BAL and mini-BAL, to determine the mini-BAL's diagnostic accuracy. Methods: We conducted a systematic review searching the databases PubMed (MEDLINE), EMBASE, Cochrane Library, Scopus, and clinicaltrials.gov from inception until January 2022, in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Search terms included variations on "pneumonia," "critical illness," and "mini-bronchoalveolar lavage." Article screening and data extraction were performed independently by 2 reviewers. Results: Our search yielded 4296 abstracts. This was narrowed to 6 studies in which each patient underwent both mini-BAL and bronchoscopic BAL in succession. Included patients had a mean APACHE II score of 20.02 ± 3.81 and 15.95 ± 11.46 ventilator days. The sensitivity of the mini-BAL for diagnosis of pneumonia was 0.90 (95% confidence interval [CI]: 0.778-1.000) and the specificity was 0.827 (95% CI: 0.716-0.938). Limitations included inconsistency in volume of saline instilled and heterogeneity in included patients Conclusion: This study is the first to compile data from multiple publications directly comparing the mini-BAL to bronchoscopic BAL for diagnosing pneumonia in ventilated patients. Our data demonstrate a high degree of both sensitivity and specificity of mini-BAL for the diagnosis of pneumonia in ventilated patients and indicate that mini-BAL could be considered as an acceptable alternative diagnostic study.

Erratum: Addition to "Stereo-Aware Extension of HOSE Codes".

[This corrects the article DOI: 10.1021/acsomega.9b00488.].

Depression, Anxiety, and Stress among Hangover-Sensitive and Hangover-Resistant Drinkers.

This study investigated potential differences in baseline (i.e., non-hangover-related) levels of depression, anxiety, and stress between individuals who are sensitive to and those resistant to hangovers after consuming alcohol. Participants included 5111 university students from the Netherlands and the U.K., including 3205 hangover-sensitive and 1906 hangover-resistant drinkers. All participants completed surveys on their demographics, alcohol consumption, and hangover susceptibility (whether they experienced a hangover in the past 12 months), as well as their baseline levels of depression, anxiety, and stress on the DASS-21 scale. The results showed that hangover-sensitive drinkers had significantly higher levels of anxiety and stress, but not depression, compared to hangover-resistant drinkers. However, the observed differences between the two groups were small, with a magnitude of less than 1 out of 42 points on the DASS-21 anxiety and stress subscales, and are thus unlikely to be clinically meaningful.

Standing up for Myself (STORM): Adapting and piloting a web-delivered psychosocial group intervention for people with intellectual disabilities.

BACKGROUND: Our STORM intervention was developed for people (16 +) with intellectual disabilities to enhance their capacity to manage and resist stigma. The current study describes the adaptation of STORM for (synchronous) on-line delivery in the context of the Covid-19 pandemic. AIMS: To adapt the manualised face-to-face STORM group intervention for delivery via web-based meeting platforms and to conduct an initial pilot study to consider its acceptability and feasibility. METHODS AND PROCEDURES: The 5-session STORM intervention was carefully adapted for online delivery. In a pilot study with four community groups (N = 22), outcome, health economics and attendance data were collected, and fidelity of delivery assessed. Focus groups with participants, and interviews with facilitators provided data on acceptability and feasibility. OUTCOMES AND RESULTS: The intervention was adapted with minimal changes to the content required. In the pilot study, 95% of participants were retained at follow-up, 91% attended at least three of the five sessions. Outcome measure completion and fidelity were excellent, and facilitators reported implementation to be feasible. The intervention was reported to be acceptable by participants. CONCLUSIONS AND IMPLICATIONS: When provided with the necessary resources and support, people with intellectual disabilities participate actively in web-delivered group interventions.

Cirrhotic cardiomyopathy: Predictors of major adverse cardiac events and assessment of reversibility after liver transplant.

BACKGROUND: Major adverse cardiac events (MACE) are a leading cause of morbidity and mortality after orthotopic liver transplantation (OLT). Cirrhotic cardiomyopathy (CCM), initially described in 2005 and revised in 2019, is a source of MACE in patients after OLT. We sought to identify CCM-related predictors of MACE at one-year follow-up after OLT and assess for reversibility of CCM post-OLT. METHODS: This is a retrospective study of adult patients who underwent OLT between 2009 and 2019. All patients had transthoracic echocardiography pre-and post-OLT. Patients with a left ventricular ejection fraction <50 % pre-OLT were excluded. MACE was defined as death, myocardial infarction, congestive heart failure hospitalization, or cardiac arrest. RESULTS: In total, 131 patients were included in this study, of whom 103 and 23 patients met the 2005 and 2019 criteria, respectively. During the follow-up period, 42 patients had MACE and these patients were more likely to have ascites (p = 0.003), hepatorenal syndrome (p = 0.019), and CCM per 2005 criteria (p = 0.023). There were no significant differences between pre-OLT CCM per 2019 criteria (19 % vs 17 %, p = 0.758) or MELD-Na score (21.24 vs 19.40, p = 0.166) for MACE post-OLT. Per the 2005 criteria, 35 of 103 patients recovered and these patients were less likely to have MACE post-OLT (p = 0.012). Per the 2019 criteria, 13 of 23 patients recovered post-OLT but this low number precluded further statistics. CONCLUSION: The 2005 Montreal criteria for CCM were an independent predictor of MACE at one-year follow-up post-OLT while the 2019 CCC criteria for CCM were not. In addition, the 2005 Montreal criteria were more prevalent when compared to 2019 CCC criteria. Finally, the 2005 Montreal criteria were reversible post-OLT 34 % of the time compared to the 2019 CCC criteria which were reversible 57 % of the time.

Quantification of localized NAD+ changes reveals unique specificity of NAD+ regulation in the hypothalamus.

Recently, it has become a consensus that systemic decreases in NAD+ are a critical trigger for age-associated functional decline in multiple tissues and organs. The hypothalamus, which contains several functionally distinct subregions called nuclei, functions as a high-order control center of aging in mammals. However, due to a technical difficulty, how NAD+ levels change locally in each hypothalamic nucleus during aging remains uninvestigated. We were able to establish a new combinatorial methodology, using laser-captured microdissection (LCM) and high-performance liquid chromatography (HPLC), to accurately measure NAD+ levels in small tissue samples. We applied this methodology to examine local NAD+ changes in hypothalamic nuclei and found that NAD+ levels were decreased significantly in the arcuate nucleus (ARC), ventromedial hypothalamus (VMH), and lateral hypothalamus (LH), but not in the dorsomedial hypothalamus (DMH) of 22-month-old mice, compared to those of 3-month-old mice. The administration of nicotinamide mononucleotide (NMN) significantly increased NAD+ levels in all these hypothalamic nuclei. Interestingly, the administration of extracellular nicotinamide phosphoribosyltransferase-containing extracellular vesicles (eNampt-EVs) purified from young mice increased NAD+ levels in the ARC and DMH. These results reveal the unique specificity of NAD+ regulation in the hypothalamus during aging.